HEADER HYDROLASE 15-APR-18 6GBJ TITLE REPERTOIRES OF FUNCTIONALLY DIVERSE ENZYMES THROUGH COMPUTATIONAL TITLE 2 DESIGN AT EPISTATIC ACTIVE-SITE POSITIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARATHION HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOTRIESTERASE,PTE; COMPND 5 EC: 3.1.8.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BREVUNDIMONAS DIMINUTA; SOURCE 3 ORGANISM_COMMON: PSEUDOMONAS DIMINUTA; SOURCE 4 ORGANISM_TAXID: 293; SOURCE 5 GENE: OPD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOTRIESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR O.KHERSONSKY,R.LIPSH,Z.AVIZEMER,M.GOLDSMITH,Y.ASHANI,H.LEADER,O.DYM, AUTHOR 2 S.ROGOTNER,D.TRUDEAU,D.S.TAWFIK,S.J.FLEISHMAN REVDAT 2 17-JAN-24 6GBJ 1 LINK REVDAT 1 24-OCT-18 6GBJ 0 JRNL AUTH O.KHERSONSKY,R.LIPSH,Z.AVIZEMER,Y.ASHANI,M.GOLDSMITH, JRNL AUTH 2 H.LEADER,O.DYM,S.ROGOTNER,D.L.TRUDEAU,J.PRILUSKY, JRNL AUTH 3 P.AMENGUAL-RIGO,V.GUALLAR,D.S.TAWFIK,S.J.FLEISHMAN JRNL TITL AUTOMATED DESIGN OF EFFICIENT AND FUNCTIONALLY DIVERSE JRNL TITL 2 ENZYME REPERTOIRES. JRNL REF MOL. CELL V. 72 178 2018 JRNL REFN ISSN 1097-4164 JRNL PMID 30270109 JRNL DOI 10.1016/J.MOLCEL.2018.08.033 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 54923 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2889 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3955 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2546 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.257 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2649 ; 0.017 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 2380 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3584 ; 1.963 ; 1.755 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5557 ; 0.651 ; 1.719 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 333 ; 6.395 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;27.668 ;16.186 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;11.279 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.977 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3003 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 481 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1329 ; 1.434 ; 1.571 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1330 ; 1.434 ; 1.571 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1663 ; 1.929 ; 2.350 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1664 ; 1.931 ; 2.350 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1320 ; 2.902 ; 1.885 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1308 ; 2.807 ; 1.848 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1904 ; 4.035 ; 2.663 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2949 ; 4.334 ;20.572 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2915 ; 4.218 ;20.342 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6GBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009585. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57720 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 38.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04777 REMARK 200 FOR THE DATA SET : 13.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37080 REMARK 200 FOR SHELL : 2.810 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1HYZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH=7 1.7M LI2SO4, PH 7, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.01000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.74500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 139.51500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.74500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.74500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.50500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.74500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.74500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 139.51500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.74500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.74500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.50500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.01000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -168.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 69.49000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 69.49000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 93.01000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 708 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ILE A 30 REMARK 465 THR A 31 REMARK 465 ASN A 32 REMARK 465 SER A 33 REMARK 465 GLY A 34 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 36 CZ NH1 NH2 REMARK 470 ARG A 67 NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CG2 THR A 361 O ARG A 363 1.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 61 -144.38 -139.43 REMARK 500 TRP A 69 58.95 -149.29 REMARK 500 THR A 128 -165.29 -111.24 REMARK 500 TRP A 131 -154.39 -87.71 REMARK 500 GLU A 159 -131.88 54.83 REMARK 500 PHE A 306 87.86 -155.73 REMARK 500 ALA A 364 68.11 -158.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 182 0.09 SIDE CHAIN REMARK 500 ARG A 363 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 HIS A 57 NE2 117.8 REMARK 620 3 ASP A 301 OD1 87.2 89.4 REMARK 620 4 FMT A 401 O2 97.8 87.8 175.0 REMARK 620 5 HOH A 530 O 110.3 131.8 91.9 86.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 201 ND1 REMARK 620 2 HIS A 230 NE2 90.3 REMARK 620 3 FMT A 401 O1 100.1 113.6 REMARK 620 4 HOH A 502 O 87.7 140.1 105.9 REMARK 620 5 HOH A 530 O 157.0 95.0 98.2 73.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 414 DBREF 6GBJ A 34 365 UNP P0A434 OPD_BREDI 34 365 SEQADV 6GBJ ILE A 30 UNP P0A434 EXPRESSION TAG SEQADV 6GBJ THR A 31 UNP P0A434 EXPRESSION TAG SEQADV 6GBJ ASN A 32 UNP P0A434 EXPRESSION TAG SEQADV 6GBJ SER A 33 UNP P0A434 EXPRESSION TAG SEQADV 6GBJ MET A 54 UNP P0A434 THR 54 ENGINEERED MUTATION SEQADV 6GBJ ASP A 77 UNP P0A434 LYS 77 ENGINEERED MUTATION SEQADV 6GBJ GLU A 111 UNP P0A434 SER 111 ENGINEERED MUTATION SEQADV 6GBJ GLU A 118 UNP P0A434 ARG 118 ENGINEERED MUTATION SEQADV 6GBJ ARG A 182 UNP P0A434 LEU 182 ENGINEERED MUTATION SEQADV 6GBJ ARG A 185 UNP P0A434 LYS 185 ENGINEERED MUTATION SEQADV 6GBJ ASP A 203 UNP P0A434 ALA 203 ENGINEERED MUTATION SEQADV 6GBJ ASP A 214 UNP P0A434 ALA 214 ENGINEERED MUTATION SEQADV 6GBJ ASP A 222 UNP P0A434 SER 222 ENGINEERED MUTATION SEQADV 6GBJ ASP A 238 UNP P0A434 SER 238 ENGINEERED MUTATION SEQADV 6GBJ ARG A 254 UNP P0A434 HIS 254 ENGINEERED MUTATION SEQADV 6GBJ TRP A 257 UNP P0A434 HIS 257 ENGINEERED MUTATION SEQADV 6GBJ ALA A 269 UNP P0A434 SER 269 ENGINEERED MUTATION SEQADV 6GBJ LEU A 274 UNP P0A434 ILE 274 ENGINEERED MUTATION SEQADV 6GBJ ALA A 293 UNP P0A434 MET 293 ENGINEERED MUTATION SEQADV 6GBJ ASP A 294 UNP P0A434 LYS 294 ENGINEERED MUTATION SEQADV 6GBJ THR A 303 UNP P0A434 LEU 303 ENGINEERED MUTATION SEQADV 6GBJ LEU A 317 UNP P0A434 MET 317 ENGINEERED MUTATION SEQADV 6GBJ ASP A 343 UNP P0A434 GLN 343 ENGINEERED MUTATION SEQADV 6GBJ GLU A 347 UNP P0A434 ALA 347 ENGINEERED MUTATION SEQADV 6GBJ THR A 348 UNP P0A434 GLY 348 ENGINEERED MUTATION SEQADV 6GBJ MET A 350 UNP P0A434 THR 350 ENGINEERED MUTATION SEQADV 6GBJ ASP A 352 UNP P0A434 THR 352 ENGINEERED MUTATION SEQRES 1 A 336 ILE THR ASN SER GLY ASP ARG ILE ASN THR VAL ARG GLY SEQRES 2 A 336 PRO ILE THR ILE SER GLU ALA GLY PHE THR LEU MET HIS SEQRES 3 A 336 GLU HIS ILE CYS GLY SER SER ALA GLY PHE LEU ARG ALA SEQRES 4 A 336 TRP PRO GLU PHE PHE GLY SER ARG ASP ALA LEU ALA GLU SEQRES 5 A 336 LYS ALA VAL ARG GLY LEU ARG ARG ALA ARG ALA ALA GLY SEQRES 6 A 336 VAL ARG THR ILE VAL ASP VAL SER THR PHE ASP ILE GLY SEQRES 7 A 336 ARG ASP VAL GLU LEU LEU ALA GLU VAL SER GLU ALA ALA SEQRES 8 A 336 ASP VAL HIS ILE VAL ALA ALA THR GLY LEU TRP PHE ASP SEQRES 9 A 336 PRO PRO LEU SER MET ARG LEU ARG SER VAL GLU GLU LEU SEQRES 10 A 336 THR GLN PHE PHE LEU ARG GLU ILE GLN TYR GLY ILE GLU SEQRES 11 A 336 ASP THR GLY ILE ARG ALA GLY ILE ILE LYS VAL ALA THR SEQRES 12 A 336 THR GLY LYS ALA THR PRO PHE GLN GLU ARG VAL LEU ARG SEQRES 13 A 336 ALA ALA ALA ARG ALA SER LEU ALA THR GLY VAL PRO VAL SEQRES 14 A 336 THR THR HIS THR ASP ALA SER GLN ARG ASP GLY GLU GLN SEQRES 15 A 336 GLN ALA ASP ILE PHE GLU SER GLU GLY LEU ASP PRO SER SEQRES 16 A 336 ARG VAL CYS ILE GLY HIS SER ASP ASP THR ASP ASP LEU SEQRES 17 A 336 ASP TYR LEU THR ALA LEU ALA ALA ARG GLY TYR LEU ILE SEQRES 18 A 336 GLY LEU ASP ARG ILE PRO TRP SER ALA ILE GLY LEU GLU SEQRES 19 A 336 ASP ASN ALA SER ALA ALA ALA LEU LEU GLY LEU ARG SER SEQRES 20 A 336 TRP GLN THR ARG ALA LEU LEU ILE LYS ALA LEU ILE ASP SEQRES 21 A 336 GLN GLY TYR ALA ASP GLN ILE LEU VAL SER ASN ASP TRP SEQRES 22 A 336 THR PHE GLY PHE SER SER TYR VAL THR ASN ILE MET ASP SEQRES 23 A 336 VAL LEU ASP ARG VAL ASN PRO ASP GLY MET ALA PHE ILE SEQRES 24 A 336 PRO LEU ARG VAL ILE PRO PHE LEU ARG GLU LYS GLY VAL SEQRES 25 A 336 PRO ASP GLU THR LEU GLU THR ILE MET VAL ASP ASN PRO SEQRES 26 A 336 ALA ARG PHE LEU SER PRO THR LEU ARG ALA SER HET FMT A 401 3 HET ZN A 402 1 HET ZN A 403 1 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET SO4 A 412 5 HET SO4 A 413 5 HET SO4 A 414 5 HETNAM FMT FORMIC ACID HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 FMT C H2 O2 FORMUL 3 ZN 2(ZN 2+) FORMUL 5 EDO 8(C2 H6 O2) FORMUL 13 SO4 3(O4 S 2-) FORMUL 16 HOH *227(H2 O) HELIX 1 AA1 SER A 47 ALA A 49 5 3 HELIX 2 AA2 GLY A 64 TRP A 69 1 6 HELIX 3 AA3 PRO A 70 GLY A 74 5 5 HELIX 4 AA4 SER A 75 ALA A 93 1 19 HELIX 5 AA5 THR A 103 GLY A 107 5 5 HELIX 6 AA6 ASP A 109 ASP A 121 1 13 HELIX 7 AA7 PRO A 135 LEU A 140 1 6 HELIX 8 AA8 SER A 142 TYR A 156 1 15 HELIX 9 AA9 THR A 177 GLY A 195 1 19 HELIX 10 AB1 ASP A 203 GLN A 206 5 4 HELIX 11 AB2 ARG A 207 GLU A 219 1 13 HELIX 12 AB3 ASP A 222 SER A 224 5 3 HELIX 13 AB4 HIS A 230 THR A 234 5 5 HELIX 14 AB5 ASP A 236 ARG A 246 1 11 HELIX 15 AB6 ASN A 265 GLY A 273 1 9 HELIX 16 AB7 SER A 276 GLN A 290 1 15 HELIX 17 AB8 TYR A 292 ASP A 294 5 3 HELIX 18 AB9 ASN A 312 ASN A 321 1 10 HELIX 19 AC1 ASP A 323 MET A 325 5 3 HELIX 20 AC2 ALA A 326 ARG A 331 1 6 HELIX 21 AC3 ARG A 331 LYS A 339 1 9 HELIX 22 AC4 PRO A 342 VAL A 351 1 10 HELIX 23 AC5 VAL A 351 SER A 359 1 9 SHEET 1 AA1 2 ARG A 36 THR A 39 0 SHEET 2 AA1 2 GLY A 42 THR A 45 -1 O ILE A 44 N ILE A 37 SHEET 1 AA2 3 THR A 52 GLU A 56 0 SHEET 2 AA2 3 THR A 97 ASP A 100 1 O VAL A 99 N LEU A 53 SHEET 3 AA2 3 HIS A 123 VAL A 125 1 O HIS A 123 N ILE A 98 SHEET 1 AA3 6 ALA A 127 GLY A 129 0 SHEET 2 AA3 6 ILE A 167 ALA A 171 1 O LYS A 169 N THR A 128 SHEET 3 AA3 6 VAL A 198 HIS A 201 1 O THR A 199 N ILE A 168 SHEET 4 AA3 6 VAL A 226 ILE A 228 1 O CYS A 227 N VAL A 198 SHEET 5 AA3 6 LEU A 249 LEU A 252 1 O LEU A 249 N ILE A 228 SHEET 6 AA3 6 ILE A 296 VAL A 298 1 O LEU A 297 N LEU A 252 LINK NZ LYS A 169 C FMT A 401 1555 1555 1.36 LINK NE2 HIS A 55 ZN ZN A 402 1555 1555 2.06 LINK NE2 HIS A 57 ZN ZN A 402 1555 1555 2.04 LINK ND1 HIS A 201 ZN ZN A 403 1555 1555 2.12 LINK NE2 HIS A 230 ZN ZN A 403 1555 1555 2.08 LINK OD1 ASP A 301 ZN ZN A 402 1555 1555 2.19 LINK O2 FMT A 401 ZN ZN A 402 1555 1555 2.14 LINK O1 FMT A 401 ZN ZN A 403 1555 1555 1.97 LINK ZN ZN A 402 O HOH A 530 1555 1555 2.00 LINK ZN ZN A 403 O HOH A 502 1555 1555 2.10 LINK ZN ZN A 403 O HOH A 530 1555 1555 2.18 SITE 1 AC1 10 HIS A 55 HIS A 57 TRP A 131 LYS A 169 SITE 2 AC1 10 HIS A 201 HIS A 230 ZN A 402 ZN A 403 SITE 3 AC1 10 EDO A 405 HOH A 530 SITE 1 AC2 7 HIS A 55 HIS A 57 ASP A 301 FMT A 401 SITE 2 AC2 7 ZN A 403 EDO A 405 HOH A 530 SITE 1 AC3 8 HIS A 201 HIS A 230 ARG A 254 FMT A 401 SITE 2 AC3 8 ZN A 402 EDO A 405 HOH A 502 HOH A 530 SITE 1 AC4 8 HIS A 57 GLY A 60 TRP A 257 ASP A 301 SITE 2 AC4 8 THR A 303 PHE A 306 EDO A 405 HOH A 526 SITE 1 AC5 10 HIS A 57 TRP A 131 FMT A 401 ZN A 402 SITE 2 AC5 10 ZN A 403 EDO A 404 EDO A 407 HOH A 502 SITE 3 AC5 10 HOH A 526 HOH A 530 SITE 1 AC6 7 TYR A 156 GLY A 157 ILE A 158 GLU A 159 SITE 2 AC6 7 ASP A 160 THR A 161 GLY A 162 SITE 1 AC7 7 TRP A 131 HIS A 201 ARG A 254 EDO A 405 SITE 2 AC7 7 HOH A 502 HOH A 503 HOH A 529 SITE 1 AC8 8 PRO A 70 SER A 75 ARG A 76 ASP A 77 SITE 2 AC8 8 ARG A 363 HOH A 506 HOH A 680 HOH A 701 SITE 1 AC9 7 ASP A 233 ARG A 254 LEU A 271 LEU A 272 SITE 2 AC9 7 ARG A 280 HOH A 598 HOH A 608 SITE 1 AD1 4 LYS A 175 ALA A 176 GLU A 181 GLN A 211 SITE 1 AD2 7 PRO A 256 TRP A 277 VAL A 320 ASN A 321 SITE 2 AD2 7 PHE A 327 HOH A 578 HOH A 584 SITE 1 AD3 4 LYS A 82 ARG A 85 ARG A 89 HOH A 537 SITE 1 AD4 2 TRP A 277 GLN A 278 SITE 1 AD5 3 ARG A 139 HOH A 549 HOH A 582 CRYST1 69.490 69.490 186.020 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005376 0.00000